Starting phenix.real_space_refine on Wed Aug 5 21:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl3_49516/08_2026/9nl3_49516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl3_49516/08_2026/9nl3_49516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nl3_49516/08_2026/9nl3_49516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl3_49516/08_2026/9nl3_49516.map" model { file = "/net/cci-nas-00/data/ceres_data/9nl3_49516/08_2026/9nl3_49516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl3_49516/08_2026/9nl3_49516.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 159 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 6993 2.51 5 N 2165 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11939 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8655 Classifications: {'peptide': 1079} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1028} Chain breaks: 2 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "P" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1140 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 24, 'rna3p_pyr': 17} Link IDs: {'rna2p': 12, 'rna3p': 40} Chain breaks: 2 Chain: "T" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1052 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 310 SG CYS A 41 55.775 30.513 64.736 1.00 86.53 S ATOM 330 SG CYS A 44 58.211 31.927 62.111 1.00 93.20 S ATOM 465 SG CYS A 61 54.773 31.941 61.304 1.00 82.06 S ATOM 579 SG CYS A 76 76.412 46.802 52.258 1.00 97.02 S ATOM 601 SG CYS A 79 74.639 44.489 54.904 1.00 89.57 S ATOM 7222 SG CYS A 991 31.997 32.857 97.447 1.00 79.38 S ATOM 7249 SG CYS A 994 28.609 32.222 98.899 1.00 63.53 S ATOM 7348 SG CYS A1008 31.554 33.293 101.124 1.00 79.09 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' TTP A1206 " occ=0.65 ... (27 atoms not shown) pdb=" PG TTP A1206 " occ=0.65 Time building chain proxies: 2.70, per 1000 atoms: 0.23 Number of scatterers: 11939 At special positions: 0 Unit cell: (122.616, 119.472, 139.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 51 16.00 P 159 15.00 Mg 1 11.99 O 2566 8.00 N 2165 7.00 C 6993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 13 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 483.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 32 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 27 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 57 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 61 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 44 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 41 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 92 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 97 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 76 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 79 " pdb=" ZN A1204 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A1003 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 991 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 994 " pdb="ZN ZN A1204 " - pdb=" SG CYS A1008 " Number of angles added : 8 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 56.1% alpha, 8.7% beta 55 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 50 through 58 removed outlier: 3.582A pdb=" N VAL A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.749A pdb=" N GLN A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.622A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.230A pdb=" N SER A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.700A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.671A pdb=" N GLU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 304 removed outlier: 5.159A pdb=" N CYS A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.876A pdb=" N ARG A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.692A pdb=" N ASP A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.844A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.587A pdb=" N ARG A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.826A pdb=" N ASN A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.663A pdb=" N PHE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 547 removed outlier: 3.523A pdb=" N LEU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 619 through 640 removed outlier: 4.691A pdb=" N LEU A 623 " --> pdb=" O PRO A 619 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 667 through 684 Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.526A pdb=" N THR A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 removed outlier: 3.582A pdb=" N LEU A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR A 781 " --> pdb=" O PRO A 777 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.347A pdb=" N LEU A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.832A pdb=" N GLY A 826 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.623A pdb=" N PHE A 859 " --> pdb=" O MET A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 876 Processing helix chain 'A' and resid 919 through 931 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 948 through 953 removed outlier: 3.881A pdb=" N GLN A 952 " --> pdb=" O ASN A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.665A pdb=" N THR A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'A' and resid 1000 through 1007 removed outlier: 3.604A pdb=" N ILE A1005 " --> pdb=" O CYS A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.531A pdb=" N LYS A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1091 removed outlier: 3.651A pdb=" N GLU A1081 " --> pdb=" O SER A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 3.546A pdb=" N HIS A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1130 removed outlier: 3.950A pdb=" N LEU A1126 " --> pdb=" O ASP A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1168 removed outlier: 3.569A pdb=" N ASP A1154 " --> pdb=" O PHE A1150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A1168 " --> pdb=" O ARG A1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.725A pdb=" N TRP A 74 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 495 removed outlier: 7.345A pdb=" N CYS A 469 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N THR A 598 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 471 " --> pdb=" O THR A 598 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 595 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.920A pdb=" N LEU A 659 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 693 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.920A pdb=" N LEU A 659 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 693 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 694 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 3.633A pdb=" N TYR A 643 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 713 through 714 removed outlier: 3.513A pdb=" N ILE A 714 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 717 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 730 Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1037 removed outlier: 6.024A pdb=" N ALA A1063 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A1109 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A1065 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A1111 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP A1067 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A1113 " --> pdb=" O ASP A1067 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A1069 " --> pdb=" O LEU A1113 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1921 1.33 - 1.45: 3907 1.45 - 1.57: 6293 1.57 - 1.69: 312 1.69 - 1.82: 71 Bond restraints: 12504 Sorted by residual: bond pdb=" C1' DC T 9 " pdb=" N1 DC T 9 " ideal model delta sigma weight residual 1.468 1.353 0.115 1.40e-02 5.10e+03 6.69e+01 bond pdb=" C1' DC B 61 " pdb=" N1 DC B 61 " ideal model delta sigma weight residual 1.468 1.574 -0.106 1.40e-02 5.10e+03 5.72e+01 bond pdb=" O3B TTP A1206 " pdb=" PG TTP A1206 " ideal model delta sigma weight residual 1.748 1.612 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C4 DC T 9 " pdb=" N4 DC T 9 " ideal model delta sigma weight residual 1.335 1.280 0.055 9.00e-03 1.23e+04 3.74e+01 bond pdb=" C5 DC T 9 " pdb=" C6 DC T 9 " ideal model delta sigma weight residual 1.339 1.297 0.042 8.00e-03 1.56e+04 2.76e+01 ... (remaining 12499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.50: 17572 8.50 - 17.01: 5 17.01 - 25.51: 3 25.51 - 34.02: 5 34.02 - 42.52: 4 Bond angle restraints: 17589 Sorted by residual: angle pdb=" OP1 DG T 12 " pdb=" P DG T 12 " pdb=" OP2 DG T 12 " ideal model delta sigma weight residual 120.00 77.48 42.52 3.00e+00 1.11e-01 2.01e+02 angle pdb=" OP1 DC B 57 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 120.00 80.08 39.92 3.00e+00 1.11e-01 1.77e+02 angle pdb=" O3' DC T 11 " pdb=" P DG T 12 " pdb=" OP2 DG T 12 " ideal model delta sigma weight residual 108.00 70.89 37.11 3.00e+00 1.11e-01 1.53e+02 angle pdb=" OP2 DC B 57 " pdb=" P DC B 57 " pdb=" O5' DC B 57 " ideal model delta sigma weight residual 108.00 73.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP1 DC B 57 " ideal model delta sigma weight residual 108.00 78.06 29.94 3.00e+00 1.11e-01 9.96e+01 ... (remaining 17584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 6610 35.85 - 71.70: 738 71.70 - 107.56: 29 107.56 - 143.41: 2 143.41 - 179.26: 11 Dihedral angle restraints: 7390 sinusoidal: 4244 harmonic: 3146 Sorted by residual: dihedral pdb=" O4' U R 54 " pdb=" C1' U R 54 " pdb=" N1 U R 54 " pdb=" C2 U R 54 " ideal model delta sinusoidal sigma weight residual -128.00 51.26 -179.26 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CD ARG A 166 " pdb=" NE ARG A 166 " pdb=" CZ ARG A 166 " pdb=" NH1 ARG A 166 " ideal model delta sinusoidal sigma weight residual 0.00 60.34 -60.34 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASN A 142 " pdb=" C ASN A 142 " pdb=" N LYS A 143 " pdb=" CA LYS A 143 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 7387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1995 0.409 - 0.819: 0 0.819 - 1.228: 0 1.228 - 1.638: 0 1.638 - 2.047: 1 Chirality restraints: 1996 Sorted by residual: chirality pdb=" P DT B 35 " pdb=" OP1 DT B 35 " pdb=" OP2 DT B 35 " pdb=" O5' DT B 35 " both_signs ideal model delta sigma weight residual True 2.34 0.29 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" P DC B 57 " pdb=" OP1 DC B 57 " pdb=" OP2 DC B 57 " pdb=" O5' DC B 57 " both_signs ideal model delta sigma weight residual True 2.34 2.04 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1' DG B 60 " pdb=" O4' DG B 60 " pdb=" C2' DG B 60 " pdb=" N9 DG B 60 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1993 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " -0.966 9.50e-02 1.11e+02 4.33e-01 1.13e+02 pdb=" NE ARG A 166 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 9 " -0.054 2.00e-02 2.50e+03 3.88e-02 3.38e+01 pdb=" N1 DC T 9 " 0.031 2.00e-02 2.50e+03 pdb=" C2 DC T 9 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DC T 9 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC T 9 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC T 9 " 0.063 2.00e-02 2.50e+03 pdb=" N4 DC T 9 " -0.067 2.00e-02 2.50e+03 pdb=" C5 DC T 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC T 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG B 62 " -0.021 2.00e-02 2.50e+03 3.04e-02 2.78e+01 pdb=" N9 DG B 62 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DG B 62 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG B 62 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DG B 62 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG B 62 " 0.061 2.00e-02 2.50e+03 pdb=" O6 DG B 62 " -0.051 2.00e-02 2.50e+03 pdb=" N1 DG B 62 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG B 62 " 0.045 2.00e-02 2.50e+03 pdb=" N2 DG B 62 " -0.044 2.00e-02 2.50e+03 pdb=" N3 DG B 62 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG B 62 " -0.001 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 67 2.46 - 3.07: 7937 3.07 - 3.68: 20016 3.68 - 4.29: 29768 4.29 - 4.90: 45536 Nonbonded interactions: 103324 Sorted by model distance: nonbonded pdb="MG MG A1205 " pdb=" O1A TTP A1206 " model vdw 1.847 2.170 nonbonded pdb=" OG SER A 933 " pdb=" OP1 DA B 31 " model vdw 1.953 3.040 nonbonded pdb=" OH TYR A 257 " pdb=" O PHE A 407 " model vdw 2.011 3.040 nonbonded pdb=" OH TYR A 774 " pdb=" OP2 DG P 20 " model vdw 2.031 3.040 nonbonded pdb=" O VAL A1097 " pdb=" OG1 THR A1101 " model vdw 2.083 3.040 ... (remaining 103319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 12519 Z= 0.446 Angle : 1.145 42.521 17599 Z= 0.651 Chirality : 0.069 2.047 1996 Planarity : 0.012 0.433 1680 Dihedral : 24.639 179.259 5341 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.71 % Favored : 92.82 % Rotamer: Outliers : 0.63 % Allowed : 21.72 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.26), residues: 1073 helix: -0.02 (0.24), residues: 505 sheet: -2.42 (0.51), residues: 92 loop : -1.61 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 490 TYR 0.018 0.001 TYR A 256 PHE 0.013 0.001 PHE A1150 TRP 0.007 0.001 TRP A 541 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.45 (12504) covalent geometry : angle 1.14092 / 0.65 (17589) SS BOND : bond 0.00242 / 0.13 ( 1) SS BOND : angle 1.61895 / 0.88 ( 2) hydrogen bonds : bond 0.14131 / 8.83 ( 547) hydrogen bonds : angle 6.78496 / 4.84 ( 1481) metal coordination : bond 0.01226 / 0.80 ( 14) metal coordination : angle 4.89862 / 2.45 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: -0.0412 (OUTLIER) cc_final: -0.1224 (ptp90) REVERT: A 669 MET cc_start: 0.8956 (tpp) cc_final: 0.8611 (tpp) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1175 time to fit residues: 14.3498 Evaluate side-chains 84 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104822 restraints weight = 18829.322| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.84 r_work: 0.3184 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12519 Z= 0.232 Angle : 1.090 40.008 17599 Z= 0.485 Chirality : 0.069 2.036 1996 Planarity : 0.006 0.104 1680 Dihedral : 26.160 177.052 3142 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.87 % Favored : 93.76 % Rotamer: Outliers : 3.04 % Allowed : 21.51 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.26), residues: 1073 helix: 0.07 (0.23), residues: 533 sheet: -2.25 (0.49), residues: 94 loop : -1.45 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 165 TYR 0.017 0.002 TYR A 377 PHE 0.015 0.002 PHE A1159 TRP 0.021 0.002 TRP A 489 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (12504) covalent geometry : angle 1.08839 / 0.49 (17589) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 1.28891 / 0.71 ( 2) hydrogen bonds : bond 0.06259 / 4.13 ( 547) hydrogen bonds : angle 4.96922 / 3.54 ( 1481) metal coordination : bond 0.01551 / 1.12 ( 14) metal coordination : angle 3.33102 / 1.72 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: -0.0955 (OUTLIER) cc_final: -0.1263 (mtm-85) REVERT: A 291 ASN cc_start: 0.7474 (m-40) cc_final: 0.7178 (m-40) REVERT: A 329 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7193 (mm-40) REVERT: A 377 TYR cc_start: 0.8093 (t80) cc_final: 0.7891 (t80) REVERT: A 465 MET cc_start: 0.8265 (ptm) cc_final: 0.7919 (ptt) REVERT: A 691 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8330 (mmmt) REVERT: A 989 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8185 (mtmt) outliers start: 29 outliers final: 10 residues processed: 107 average time/residue: 0.1131 time to fit residues: 16.9067 Evaluate side-chains 90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 20.0000 chunk 86 optimal weight: 0.2980 chunk 118 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 670 ASN A 993 HIS A1099 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109307 restraints weight = 18991.115| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.85 r_work: 0.3251 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12519 Z= 0.145 Angle : 1.019 39.963 17599 Z= 0.445 Chirality : 0.068 2.225 1996 Planarity : 0.005 0.041 1680 Dihedral : 25.873 179.428 3141 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.38 % Favored : 95.25 % Rotamer: Outliers : 2.94 % Allowed : 22.35 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1073 helix: 0.49 (0.23), residues: 525 sheet: -1.91 (0.48), residues: 95 loop : -1.31 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 956 TYR 0.014 0.001 TYR A 256 PHE 0.015 0.001 PHE A1150 TRP 0.012 0.001 TRP A 489 HIS 0.010 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (12504) covalent geometry : angle 1.01786 / 0.45 (17589) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 1.22390 / 0.68 ( 2) hydrogen bonds : bond 0.05435 / 3.53 ( 547) hydrogen bonds : angle 4.58050 / 3.25 ( 1481) metal coordination : bond 0.00507 / 0.32 ( 14) metal coordination : angle 2.51754 / 1.20 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8099 (mp0) cc_final: 0.7805 (mp0) REVERT: A 145 ILE cc_start: 0.2999 (OUTLIER) cc_final: 0.2569 (mt) REVERT: A 291 ASN cc_start: 0.7427 (m-40) cc_final: 0.7198 (m-40) REVERT: A 329 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: A 441 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7604 (tttt) REVERT: A 465 MET cc_start: 0.8215 (ptm) cc_final: 0.7879 (ptt) REVERT: A 691 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8531 (mmmt) REVERT: A 736 ASP cc_start: 0.8942 (t0) cc_final: 0.8723 (t70) outliers start: 28 outliers final: 13 residues processed: 108 average time/residue: 0.1125 time to fit residues: 17.1750 Evaluate side-chains 95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 0.0060 chunk 83 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.148416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108243 restraints weight = 18952.436| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.89 r_work: 0.3236 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12519 Z= 0.151 Angle : 1.015 39.600 17599 Z= 0.439 Chirality : 0.067 2.190 1996 Planarity : 0.005 0.073 1680 Dihedral : 25.672 178.096 3137 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.03 % Favored : 94.69 % Rotamer: Outliers : 2.31 % Allowed : 23.50 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1073 helix: 0.58 (0.23), residues: 534 sheet: -1.79 (0.48), residues: 95 loop : -1.28 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 956 TYR 0.023 0.001 TYR A 377 PHE 0.012 0.001 PHE A1159 TRP 0.006 0.001 TRP A 541 HIS 0.003 0.001 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (12504) covalent geometry : angle 1.01422 / 0.44 (17589) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 1.20064 / 0.67 ( 2) hydrogen bonds : bond 0.05018 / 3.31 ( 547) hydrogen bonds : angle 4.42744 / 3.14 ( 1481) metal coordination : bond 0.00662 / 0.48 ( 14) metal coordination : angle 1.98920 / 0.97 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7451 (mmt) cc_final: 0.7206 (tpt) REVERT: A 26 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 77 GLU cc_start: 0.8077 (mp0) cc_final: 0.7719 (mp0) REVERT: A 329 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7152 (mm-40) REVERT: A 441 LYS cc_start: 0.8160 (mmpt) cc_final: 0.7525 (mptt) REVERT: A 465 MET cc_start: 0.8264 (ptm) cc_final: 0.7949 (ptt) REVERT: A 691 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8353 (mmmt) outliers start: 22 outliers final: 13 residues processed: 101 average time/residue: 0.1073 time to fit residues: 15.5662 Evaluate side-chains 93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106086 restraints weight = 18780.752| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.83 r_work: 0.3198 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12519 Z= 0.191 Angle : 1.029 39.300 17599 Z= 0.446 Chirality : 0.066 2.117 1996 Planarity : 0.005 0.051 1680 Dihedral : 25.600 176.562 3135 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 3.57 % Allowed : 23.50 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.26), residues: 1073 helix: 0.56 (0.23), residues: 535 sheet: -1.75 (0.49), residues: 97 loop : -1.22 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 165 TYR 0.012 0.002 TYR A 953 PHE 0.014 0.002 PHE A1159 TRP 0.008 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (12504) covalent geometry : angle 1.02845 / 0.45 (17589) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 1.06868 / 0.59 ( 2) hydrogen bonds : bond 0.05037 / 3.35 ( 547) hydrogen bonds : angle 4.39138 / 3.11 ( 1481) metal coordination : bond 0.01316 / 0.97 ( 14) metal coordination : angle 2.12894 / 1.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8040 (mp0) cc_final: 0.7660 (mp0) REVERT: A 145 ILE cc_start: 0.2877 (OUTLIER) cc_final: 0.2574 (mt) REVERT: A 329 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7248 (mm-40) REVERT: A 441 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7547 (mptt) REVERT: A 669 MET cc_start: 0.8722 (tpp) cc_final: 0.8489 (tpp) REVERT: A 691 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8471 (mmmt) REVERT: A 989 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8093 (mtmt) outliers start: 34 outliers final: 17 residues processed: 109 average time/residue: 0.0975 time to fit residues: 15.3434 Evaluate side-chains 100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1012 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106063 restraints weight = 18849.662| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.85 r_work: 0.3202 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12519 Z= 0.177 Angle : 1.018 39.480 17599 Z= 0.439 Chirality : 0.066 2.156 1996 Planarity : 0.005 0.047 1680 Dihedral : 25.518 176.171 3135 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 3.15 % Allowed : 24.03 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.26), residues: 1073 helix: 0.69 (0.22), residues: 537 sheet: -1.51 (0.50), residues: 97 loop : -1.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.014 0.002 TYR A 256 PHE 0.013 0.002 PHE A1159 TRP 0.008 0.001 TRP A 541 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (12504) covalent geometry : angle 1.01686 / 0.44 (17589) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 1.06239 / 0.59 ( 2) hydrogen bonds : bond 0.04809 / 3.20 ( 547) hydrogen bonds : angle 4.30128 / 3.04 ( 1481) metal coordination : bond 0.01104 / 0.80 ( 14) metal coordination : angle 2.00107 / 0.97 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8059 (mm-30) REVERT: A 77 GLU cc_start: 0.8040 (mp0) cc_final: 0.7642 (mp0) REVERT: A 145 ILE cc_start: 0.2963 (OUTLIER) cc_final: 0.2662 (mt) REVERT: A 329 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7241 (mm-40) REVERT: A 408 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7810 (mmm-85) REVERT: A 432 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7745 (p0) REVERT: A 441 LYS cc_start: 0.8216 (mmpt) cc_final: 0.7532 (mptt) REVERT: A 465 MET cc_start: 0.8385 (ptm) cc_final: 0.8027 (ptt) REVERT: A 485 ASP cc_start: 0.7328 (t0) cc_final: 0.7128 (t0) REVERT: A 490 ARG cc_start: 0.6301 (ttt90) cc_final: 0.6088 (ttt180) REVERT: A 600 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8336 (tttp) REVERT: A 691 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8465 (mmmt) REVERT: A 989 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8099 (mtmt) REVERT: A 1089 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7938 (pttt) outliers start: 30 outliers final: 22 residues processed: 103 average time/residue: 0.1113 time to fit residues: 16.2720 Evaluate side-chains 103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 117 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104572 restraints weight = 18763.707| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.85 r_work: 0.3175 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12519 Z= 0.213 Angle : 1.035 39.157 17599 Z= 0.448 Chirality : 0.066 2.107 1996 Planarity : 0.005 0.046 1680 Dihedral : 25.459 176.275 3135 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.50 % Rotamer: Outliers : 3.57 % Allowed : 23.50 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1073 helix: 0.66 (0.23), residues: 534 sheet: -1.50 (0.50), residues: 97 loop : -1.26 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.012 0.002 TYR A 953 PHE 0.014 0.002 PHE A1159 TRP 0.009 0.001 TRP A1035 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (12504) covalent geometry : angle 1.03412 / 0.45 (17589) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.97634 / 0.54 ( 2) hydrogen bonds : bond 0.04881 / 3.28 ( 547) hydrogen bonds : angle 4.32920 / 3.05 ( 1481) metal coordination : bond 0.01643 / 1.20 ( 14) metal coordination : angle 2.12151 / 1.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8044 (mp0) cc_final: 0.7627 (mp0) REVERT: A 145 ILE cc_start: 0.2914 (OUTLIER) cc_final: 0.2615 (mt) REVERT: A 329 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7279 (mm-40) REVERT: A 408 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: A 441 LYS cc_start: 0.8224 (mmpt) cc_final: 0.7562 (mptt) REVERT: A 485 ASP cc_start: 0.7427 (t0) cc_final: 0.7195 (t0) REVERT: A 600 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8433 (tttp) REVERT: A 669 MET cc_start: 0.8893 (tpp) cc_final: 0.8553 (tpp) REVERT: A 691 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8490 (mmmt) REVERT: A 743 ARG cc_start: 0.6989 (ttm-80) cc_final: 0.6692 (mtm-85) REVERT: A 989 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8120 (mtmt) REVERT: A 1089 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7915 (pttt) outliers start: 34 outliers final: 23 residues processed: 106 average time/residue: 0.1172 time to fit residues: 17.5573 Evaluate side-chains 104 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 116 optimal weight: 50.0000 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105973 restraints weight = 18768.875| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.83 r_work: 0.3200 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12519 Z= 0.162 Angle : 1.009 39.691 17599 Z= 0.434 Chirality : 0.066 2.160 1996 Planarity : 0.005 0.046 1680 Dihedral : 25.350 176.917 3135 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 3.25 % Allowed : 23.82 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.26), residues: 1073 helix: 0.72 (0.22), residues: 542 sheet: -1.23 (0.51), residues: 95 loop : -1.33 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.012 0.001 PHE A1159 TRP 0.008 0.001 TRP A1035 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (12504) covalent geometry : angle 1.00806 / 0.43 (17589) SS BOND : bond 0.00080 / 0.04 ( 1) SS BOND : angle 0.98654 / 0.55 ( 2) hydrogen bonds : bond 0.04570 / 3.07 ( 547) hydrogen bonds : angle 4.22480 / 2.98 ( 1481) metal coordination : bond 0.00915 / 0.65 ( 14) metal coordination : angle 1.91789 / 0.93 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 77 GLU cc_start: 0.8042 (mp0) cc_final: 0.7624 (mp0) REVERT: A 145 ILE cc_start: 0.3054 (OUTLIER) cc_final: 0.2772 (mt) REVERT: A 329 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7232 (mm-40) REVERT: A 408 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7732 (mmm-85) REVERT: A 441 LYS cc_start: 0.8213 (mmpt) cc_final: 0.7551 (mptt) REVERT: A 485 ASP cc_start: 0.7438 (t0) cc_final: 0.7214 (t0) REVERT: A 490 ARG cc_start: 0.6273 (ttt90) cc_final: 0.6068 (ttt180) REVERT: A 600 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8462 (tttp) REVERT: A 691 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8466 (mmmt) REVERT: A 743 ARG cc_start: 0.6988 (ttm-80) cc_final: 0.6650 (mtm-85) REVERT: A 989 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8079 (mtmt) REVERT: A 1089 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7961 (pttt) outliers start: 31 outliers final: 22 residues processed: 107 average time/residue: 0.1147 time to fit residues: 17.3727 Evaluate side-chains 103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 94 optimal weight: 0.0170 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107706 restraints weight = 18893.810| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.85 r_work: 0.3228 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12519 Z= 0.133 Angle : 0.998 39.884 17599 Z= 0.428 Chirality : 0.066 2.186 1996 Planarity : 0.004 0.045 1680 Dihedral : 25.224 177.891 3135 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 2.73 % Allowed : 24.03 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1073 helix: 0.96 (0.23), residues: 543 sheet: -1.23 (0.51), residues: 97 loop : -1.26 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.009 0.001 TYR A 953 PHE 0.026 0.001 PHE A 298 TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (12504) covalent geometry : angle 0.99768 / 0.43 (17589) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 1.04995 / 0.59 ( 2) hydrogen bonds : bond 0.04367 / 2.93 ( 547) hydrogen bonds : angle 4.12220 / 2.90 ( 1481) metal coordination : bond 0.00450 / 0.31 ( 14) metal coordination : angle 1.86561 / 0.90 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 77 GLU cc_start: 0.8039 (mp0) cc_final: 0.7639 (mp0) REVERT: A 145 ILE cc_start: 0.2978 (OUTLIER) cc_final: 0.2693 (mt) REVERT: A 329 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7249 (mm-40) REVERT: A 353 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8309 (mtm180) REVERT: A 408 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7731 (mmm-85) REVERT: A 441 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7465 (mptt) REVERT: A 485 ASP cc_start: 0.7419 (t0) cc_final: 0.7218 (t0) REVERT: A 490 ARG cc_start: 0.6225 (ttt90) cc_final: 0.6023 (ttt180) REVERT: A 600 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8383 (tttp) REVERT: A 691 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8452 (mmmt) REVERT: A 743 ARG cc_start: 0.7021 (ttm-80) cc_final: 0.6720 (mtm-85) REVERT: A 989 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: A 1089 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7934 (pttt) outliers start: 26 outliers final: 18 residues processed: 101 average time/residue: 0.1293 time to fit residues: 18.1806 Evaluate side-chains 103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1089 LYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.147438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107731 restraints weight = 18908.449| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.80 r_work: 0.3228 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12519 Z= 0.143 Angle : 0.999 39.798 17599 Z= 0.427 Chirality : 0.065 2.168 1996 Planarity : 0.004 0.046 1680 Dihedral : 25.119 177.657 3135 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 2.41 % Allowed : 24.66 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1073 helix: 0.94 (0.23), residues: 547 sheet: -1.16 (0.51), residues: 97 loop : -1.22 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.010 0.001 TYR A 953 PHE 0.014 0.001 PHE A 298 TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (12504) covalent geometry : angle 0.99894 / 0.43 (17589) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 1.14464 / 0.64 ( 2) hydrogen bonds : bond 0.04324 / 2.92 ( 547) hydrogen bonds : angle 4.09404 / 2.89 ( 1481) metal coordination : bond 0.00656 / 0.47 ( 14) metal coordination : angle 1.74720 / 0.83 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 77 GLU cc_start: 0.8045 (mp0) cc_final: 0.7644 (mp0) REVERT: A 145 ILE cc_start: 0.2771 (OUTLIER) cc_final: 0.2484 (mt) REVERT: A 329 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7261 (mm-40) REVERT: A 353 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8326 (mtm180) REVERT: A 441 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7423 (mptt) REVERT: A 485 ASP cc_start: 0.7416 (t0) cc_final: 0.7211 (t0) REVERT: A 600 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8377 (tttp) REVERT: A 691 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8460 (mmmt) REVERT: A 743 ARG cc_start: 0.7051 (ttm-80) cc_final: 0.6760 (mtm-85) REVERT: A 989 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8045 (mtmt) outliers start: 23 outliers final: 16 residues processed: 97 average time/residue: 0.1338 time to fit residues: 17.7883 Evaluate side-chains 97 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 989 LYS Chi-restraints excluded: chain A residue 1145 SER Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107885 restraints weight = 18976.790| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.84 r_work: 0.3232 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12519 Z= 0.139 Angle : 0.997 39.839 17599 Z= 0.426 Chirality : 0.065 2.177 1996 Planarity : 0.004 0.045 1680 Dihedral : 25.076 177.578 3133 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 2.10 % Allowed : 25.18 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1073 helix: 1.00 (0.23), residues: 545 sheet: -0.90 (0.51), residues: 93 loop : -1.25 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 955 TYR 0.014 0.001 TYR A 257 PHE 0.010 0.001 PHE A 83 TRP 0.011 0.001 TRP A 489 HIS 0.005 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (12504) covalent geometry : angle 0.99683 / 0.43 (17589) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 1.11890 / 0.63 ( 2) hydrogen bonds : bond 0.04262 / 2.88 ( 547) hydrogen bonds : angle 4.07063 / 2.88 ( 1481) metal coordination : bond 0.00579 / 0.41 ( 14) metal coordination : angle 1.83486 / 0.86 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.53 seconds wall clock time: 59 minutes 5.90 seconds (3545.90 seconds total)